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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-10-16 12:36:47 UTC
Update Date2022-03-07 02:49:25 UTC
HMDB IDHMDB0005009
Secondary Accession Numbers
  • HMDB0014874
  • HMDB05009
  • HMDB14874
Metabolite Identification
Common NameEsomeprazole
DescriptionEsomeprazole (brand names Nexium; Lucen; Esopral and Axagon in Italy) is a proton pump inhibitor which reduces gastric acid secretion through the inhibition of H+/K+-ATPase in gastric parietal cells. By inhibiting the functioning of this enzyme, the drug prevents the formation of gastric acid. Esomeprazole is used in the treatment of dyspepsia, peptic ulcer disease (PUD), gastroesophageal reflux disease (GORD/GERD), and Zollinger-Ellison syndrome. Esomeprazole is the S-enantiomer of omeprazole (marketed as Losec/Prilosec), and AstraZeneca claims improved efficacy of this single enantiomer product over the racemic mixture of omeprazole.
Structure
Data?1582752339
Synonyms
ValueSource
(-)-OmeprazoleChEBI
(S)-(-)-OmeprazoleChEBI
(S)-OmeprazoleChEBI
AleniaChEBI
EsczChEBI
EsofagChEBI
EsomeprazolChEBI
EsomeprazolumChEBI
Inexium paranovaChEBI
(S)-5-Methoxy-2-[[(4-methoxy-3,5-dimethyl-2-pyridinyl)methyl]sulfinyl]-1H-benzimidazoleHMDB
(S)-5-Methoxy-2-[[(4-methoxy-3,5-dimethyl-2-pyridyl)methyl]sulfinyl]-1H-benzimidazoleHMDB
Esomeprazole strontium anhydrousHMDB
Strontium, esomeprazoleHMDB
Esomeprazole sodiumHMDB
Esomeprazole strontiumHMDB
NexiumHMDB
AstraZeneca brand OF esomeprazole magnesiumHMDB
Esomeprazole magnesiumHMDB
Esomeprazole potassiumHMDB
Chemical FormulaC17H19N3O3S
Average Molecular Weight345.416
Monoisotopic Molecular Weight345.114712179
IUPAC Name5-methoxy-2-[(S)-(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole
Traditional Name5-methoxy-2-[(S)-(4-methoxy-3,5-dimethylpyridin-2-yl)methanesulfinyl]-1H-1,3-benzodiazole
CAS Registry Number119141-88-7
SMILES
COC1=CC2=C(NC(=N2)[S@@](=O)CC2=NC=C(C)C(OC)=C2C)C=C1
InChI Identifier
InChI=1S/C17H19N3O3S/c1-10-8-18-15(11(2)16(10)23-4)9-24(21)17-19-13-6-5-12(22-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)/t24-/m0/s1
InChI KeySUBDBMMJDZJVOS-DEOSSOPVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sulfinylbenzimidazoles. These are polycyclic aromatic compounds containing a sulfinyl group attached at the position 2 of a benzimidazole moiety.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzimidazoles
Sub ClassSulfinylbenzimidazoles
Direct ParentSulfinylbenzimidazoles
Alternative Parents
Substituents
  • Sulfinylbenzimidazole
  • Anisole
  • Alkyl aryl ether
  • Methylpyridine
  • Pyridine
  • Benzenoid
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Sulfoxide
  • Azacycle
  • Ether
  • Sulfinyl compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
  • 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (CHEBI:50275 )
Ontology
Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.35 g/LALOGPS
logP1.66ALOGPS
logP2.43ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)9.68ChemAxon
pKa (Strongest Basic)4.77ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area77.1 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity93.66 m³·mol⁻¹ChemAxon
Polarizability35.81 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+180.34531661259
DarkChem[M-H]-181.74331661259
DeepCCS[M+H]+183.79330932474
DeepCCS[M-H]-181.43530932474
DeepCCS[M-2H]-215.41830932474
DeepCCS[M+Na]+190.64630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
EsomeprazoleCOC1=CC2=C(NC(=N2)[S@@](=O)CC2=NC=C(C)C(OC)=C2C)C=C13958.2Standard polar33892256
EsomeprazoleCOC1=CC2=C(NC(=N2)[S@@](=O)CC2=NC=C(C)C(OC)=C2C)C=C13152.4Standard non polar33892256
EsomeprazoleCOC1=CC2=C(NC(=N2)[S@@](=O)CC2=NC=C(C)C(OC)=C2C)C=C13254.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Esomeprazole,1TMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C3141.4Semi standard non polar33892256
Esomeprazole,1TMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C2957.0Standard non polar33892256
Esomeprazole,1TMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C4039.9Standard polar33892256
Esomeprazole,1TBDMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C(C)(C)C3269.7Semi standard non polar33892256
Esomeprazole,1TBDMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C(C)(C)C3183.5Standard non polar33892256
Esomeprazole,1TBDMS,isomer #1COC1=CC=C2C(=C1)N=C([S@@](=O)CC1=NC=C(C)C(OC)=C1C)N2[Si](C)(C)C(C)(C)C4010.9Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Esomeprazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-0udj-0902000000-d7c360235f936b7123202017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Esomeprazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Esomeprazole 35V, Positive-QTOFsplash10-0f7t-0900000000-f43785dbdafca5df59962021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Esomeprazole 35V, Negative-QTOFsplash10-0006-0900000000-e0837329e37e32c98da22021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 10V, Positive-QTOFsplash10-0002-0509000000-a35086072388d122723e2016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 20V, Positive-QTOFsplash10-0002-0902000000-cf6c80499c6b8e76c5d52016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 40V, Positive-QTOFsplash10-0ul9-3900000000-2356754b2ae17bd3bc192016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 10V, Negative-QTOFsplash10-0007-0709000000-1b29375937cfcb4064142016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 20V, Negative-QTOFsplash10-002b-0900000000-3383df9e4bfd7979d5e52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 40V, Negative-QTOFsplash10-004i-0900000000-4fb7ec8321857498646d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 10V, Negative-QTOFsplash10-0007-0809000000-40107975e9855389175a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 20V, Negative-QTOFsplash10-004i-0900000000-ce24ac86003c1fd0c9152021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 40V, Negative-QTOFsplash10-004i-0900000000-7094bcd15e524be407402021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 10V, Positive-QTOFsplash10-0002-0907000000-7d804584599dc64c2e692021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 20V, Positive-QTOFsplash10-0f6t-0900000000-cd37c0cf17dabe7285d12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Esomeprazole 40V, Positive-QTOFsplash10-00m0-0900000000-c05d93e4947b35f8cede2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00736
Phenol Explorer Compound IDNot Available
FooDB IDFDB023582
KNApSAcK IDNot Available
Chemspider ID7843323
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkEsomeprazole
METLIN IDNot Available
PubChem Compound9568614
PDB IDNot Available
ChEBI ID50275
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKohl, Bernhard; Senn-Bilfinger, Joerg. Enantiomerically pure (pyridylmethylsulfinyl)benzimidazoles useful as drugs, and their preparation from racemates. Ger. Offen. (1992), 8 pp. CODEN: GWXXBX DE 4035455 A1 19920514 CAN 117:90285 AN 1992:490285
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Lind T, Rydberg L, Kyleback A, Jonsson A, Andersson T, Hasselgren G, Holmberg J, Rohss K: Esomeprazole provides improved acid control vs. omeprazole In patients with symptoms of gastro-oesophageal reflux disease. Aliment Pharmacol Ther. 2000 Jul;14(7):861-7. [PubMed:10886041 ]

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:
CYP2C19
Uniprot ID:
P33261
Molecular weight:
55944.565
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]
  2. Klotz U: Clinical impact of CYP2C19 polymorphism on the action of proton pump inhibitors: a review of a special problem. Int J Clin Pharmacol Ther. 2006 Jul;44(7):297-302. [PubMed:16961157 ]
General function:
Involved in ATP binding
Specific function:
Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
Gene Name:
ATP4A
Uniprot ID:
P20648
Molecular weight:
114117.74
References
  1. Saccar CL: The pharmacology of esomeprazole and its role in gastric acid related diseases. Expert Opin Drug Metab Toxicol. 2009 Sep;5(9):1113-24. doi: 10.1517/17425250903124363. [PubMed:19606942 ]
  2. McKeage K, Blick SK, Croxtall JD, Lyseng-Williamson KA, Keating GM: Esomeprazole: a review of its use in the management of gastric acid-related diseases in adults. Drugs. 2008;68(11):1571-607. [PubMed:18627213 ]
  3. Vachhani R, Olds G, Velanovich V: Esomeprazole: a proton pump inhibitor. Expert Rev Gastroenterol Hepatol. 2009 Feb;3(1):15-27. doi: 10.1586/17474124.3.1.15. [PubMed:19210109 ]
  4. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]